def __iter__(self):
line = self._handle.readline()
if not line.startswith(term_tag):
read_until(self._handle, term_tag)
while 1:
yield self.next()
def __iter__(self):
line = self._handle.readline()
if not line.startswith(term_tag):
read_until(self._handle, term_tag)
while 1:
yield next(self)
def __iter__(self):
fp = must_open(self.filename)
while True:
read_until(fp, "-----")
nextline = fp.readline()
nextline = fp.readline()
if not nextline.strip():
break
d = DelLine(nextline)
yield d
def __iter__(self):
fp = must_open(self.filename)
while True:
read_until(fp, "-----")
nextline = fp.readline()
nextline = fp.readline()
if not nextline.strip():
break
d = DelLine(nextline)
yield d
def __iter__(self):
line = self._handle.readline()
if not line.startswith(bac_tag):
read_until(self._handle, bac_tag)
for header, seq in read_block(self._handle, bac_tag):
rec = FpcRecord()
assert header.startswith(bac_tag)
rec.bac_name = header.split('\"')[1]
for line in seq:
if line.startswith("Map"):
rec.ctg_name = line.split('\"')[1]
if "Left" in line:
rec.map_left = line.split("Left")[1].split()[0]
rec.map_left = int(float(rec.map_left))
if "Right" in line:
rec.map_right = line.split("Right")[1].split()[0]
rec.map_right = int(float(rec.map_right))
if line.startswith("Gel_number"):
rec.gel_number = line.split()[-1]
if line.startswith("Fp_number"):
rec.fp_number = line.split()[-1]
if line.startswith("Bands"):
rec.bands = line.split()[-1]
if line.startswith("match_to_cosmid"):
rec.cosmid = line.split('\"')[1]
rec.cosmid_match = line.split("_match_")[0]
if line.startswith("Positive"):
rec.probes.append(line.split('\"')[1])
if line.startswith("Fpc_remark"):
rec.remark.append(line.split('\"')[1])
if line.startswith("Creation_date"):
rec.cre_date = line.split('_date')[1].strip()
if line.startswith("Modified_date"):
rec.mod_date = line.split('_date')[1].strip()
yield rec
def __iter__(self):
line = self._handle.readline()
if not line.startswith(bac_tag):
read_until(self._handle, bac_tag)
for header, seq in read_block(self._handle, bac_tag):
rec = FpcRecord()
assert header.startswith(bac_tag)
rec.bac_name = header.split('\"')[1]
for line in seq:
if line.startswith("Map"):
rec.ctg_name = line.split('\"')[1]
if "Left" in line:
rec.map_left = line.split("Left")[1].split()[0]
rec.map_left = int(float(rec.map_left))
if "Right" in line:
rec.map_right = line.split("Right")[1].split()[0]
rec.map_right = int(float(rec.map_right))
if line.startswith("Gel_number"):
rec.gel_number = line.split()[-1]
if line.startswith("Fp_number"):
rec.fp_number = line.split()[-1]
if line.startswith("Bands"):
rec.bands = line.split()[-1]
if line.startswith("match_to_cosmid"):
rec.cosmid = line.split('\"')[1]
rec.cosmid_match = line.split("_match_")[0]
if line.startswith("Positive"):
rec.probes.append(line.split('\"')[1])
if line.startswith("Fpc_remark"):
rec.remark.append(line.split('\"')[1])
if line.startswith("Creation_date"):
rec.cre_date = line.split('_date')[1].strip()
if line.startswith("Modified_date"):
rec.mod_date = line.split('_date')[1].strip()
yield rec
def __init__(self, fh):
line = fh.readline().strip()
self.id = line.split()[0] if line else None
read_until(fh, ">")
def __init__(self, fh):
line = fh.readline().strip()
self.id = line.split()[0] if line else None
read_until(fh, ">")
